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2012-03-23 05:30:27 -0600 commented answer Manually compiled R segfaults

@kcrisman: it tells me that I need at least 50 points of reputation to do that.

2012-03-23 03:51:59 -0600 answered a question Manually compiled R segfaults

So, it seems it is a compiler bug. Compiling on gcc 4.6 went fine with my default flags.

2012-03-15 05:17:20 -0600 commented question Manually compiled R segfaults

@kcrisman: i started bisecting the flags yesterday only to find that there's another compilation error (compiler reports bug in its own code) that shows on gcc 4.4 (which is installed on that VPS), but not on 4.5. I might find some time during the weekend to check it, but it's not a big priority to me now... I'll probably try getting gcc 4.7 on that VPS and recompile everything just to be sure. For now I use R compiled with `-O0` and it is good enough for my purposes.

2012-03-14 10:52:29 -0600 received badge  Scholar (source)
2012-03-14 10:52:29 -0600 marked best answer Sage from precompiled package -- R plots

You would need to reinstall the R spkg.

sage -f r

should do the trick.

2012-03-14 10:52:24 -0600 received badge  Supporter (source)
2012-03-14 05:04:02 -0600 commented question Manually compiled R segfaults

@kcrisman: updated. However even when launching R by itself I get a crash, and it shouldn't require much memory for itself.

2012-03-13 11:24:57 -0600 received badge  Editor (source)
2012-03-13 11:24:05 -0600 asked a question Manually compiled R segfaults

Hello,

My R crashes when I try to compile it manually. This is the output of make when trying to compile sagemath from scratch:

gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l
e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c md5.c -o md5.o
gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l
e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c signals.c -o signals.o
gcc -std=gnu99 -shared -L/home/liori/sage/sage-4.8/local/lib/ -o tools.so text.o init.o Rmd5.o md5.o signals.o -L../../../../li
make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[8]: `Makedeps' is up to date.
make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[7]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src'
make[6]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools'

 *** caught segfault ***
address 0x7fff17a1f090, cause 'memory not mapped'
aborting ...
/bin/bash: line 1:  9951 Done                    echo "tools:::.install_package_description('.', '"../../../library/tools"')"
      9952 Segmentation fault      | R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla --slave > /dev/null

Same thing when I tried to use a binary sagemath distribution and just recompile R there using ./sage -f r. When R is run as standalone binary, it crashes right after printing invitation text. I launched it with .../R --debugger gdb and printed backtrace:

[...]
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


Program received signal SIGSEGV, Segmentation fault.
strchrnul () at ../sysdeps/x86_64/strchrnul.S:34
34      ../sysdeps/x86_64/strchrnul.S: No such file or directory.
        in ../sysdeps/x86_64/strchrnul.S
Current language:  auto
The current source language is "auto; currently asm".
(gdb) bt
#0  strchrnul () at ../sysdeps/x86_64/strchrnul.S:34
#1  0x00007ffff712cd2f in __find_specmb (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, 
    ap=0x7fffffffbb80) at printf-parse.h:99
#2  _IO_vfprintf_internal (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, ap=0x7fffffffbb80)
    at vfprintf.c:1325
#3  0x00007ffff71524f2 in _IO_vsnprintf (string=0x7fffffff9b80 "", maxlen=<value optimized out>, 
    format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, args=0x7fffffffbb80) at vsnprintf.c:120
#4  0x00007ffff793671b in Rvsnprintf () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so
#5  0x00007ffff7939d5f in Rf_warning () from /home/liori/sage/sage-4.8/spkg/build/r-2 ...
(more)
2012-03-13 05:26:14 -0600 asked a question Sage from precompiled package -- R plots

Hello,

I installed Sage on my Debian Squeeze server using sage-4.8-linux-64bit-ubuntu_10.04.3_lts-x86_64-Linux.tar.lzma package. I wanted to use it mostly for R, and therefore tried some plotting, but I get the known X11 is not available message.

I installed packages recommended here in other questions, such as xorg-dev, libpango1.0-dev and libcairo2-dev, and restarted the worksheet, but with no results.

Do I need to recompile sage now?